1
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Mannar D, Saville JW, Poloni C, Zhu X, Bezeruk A, Tidey K, Ahmed S, Tuttle KS, Vahdatihassani F, Cholak S, Cook L, Steiner TS, Subramaniam S. Altered receptor binding, antibody evasion and retention of T cell recognition by the SARS-CoV-2 XBB.1.5 spike protein. Nat Commun 2024; 15:1854. [PMID: 38424106 PMCID: PMC10904792 DOI: 10.1038/s41467-024-46104-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 02/15/2024] [Indexed: 03/02/2024] Open
Abstract
The XBB.1.5 variant of SARS-CoV-2 has rapidly achieved global dominance and exhibits a high growth advantage over previous variants. Preliminary reports suggest that the success of XBB.1.5 stems from mutations within its spike glycoprotein, causing immune evasion and enhanced receptor binding. We present receptor binding studies that demonstrate retention of binding contacts with the human ACE2 receptor and a striking decrease in binding to mouse ACE2 due to the revertant R493Q mutation. Despite extensive evasion of antibody binding, we highlight a region on the XBB.1.5 spike protein receptor binding domain (RBD) that is recognized by serum antibodies from a donor with hybrid immunity, collected prior to the emergence of the XBB.1.5 variant. T cell assays reveal high frequencies of XBB.1.5 spike-specific CD4+ and CD8+ T cells amongst donors with hybrid immunity, with the CD4+ T cells skewed towards a Th1 cell phenotype and having attenuated effector cytokine secretion as compared to ancestral spike protein-specific cells. Thus, while the XBB.1.5 variant has retained efficient human receptor binding and gained antigenic alterations, it remains susceptible to recognition by T cells induced via vaccination and previous infection.
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Affiliation(s)
- Dhiraj Mannar
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - James W Saville
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Chad Poloni
- Department of Medicine and BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Xing Zhu
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Alison Bezeruk
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Keith Tidey
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Sana Ahmed
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Katharine S Tuttle
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Faezeh Vahdatihassani
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Spencer Cholak
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Laura Cook
- Department of Medicine and BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
- Department of Critical Care, Melbourne Medical School, University of Melbourne, Parkville, VIC 3010, Australia
| | - Theodore S Steiner
- Department of Medicine and BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Sriram Subramaniam
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
- Gandeeva Therapeutics, Inc., Burnaby, BC, V5C 6N5, Canada.
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2
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Cholak S, Saville JW, Zhu X, Berezuk AM, Tuttle KS, Haji-Ghassemi O, Alvarado FJ, Van Petegem F, Subramaniam S. Allosteric modulation of ryanodine receptor RyR1 by nucleotide derivatives. Structure 2023; 31:790-800.e4. [PMID: 37192614 PMCID: PMC10569317 DOI: 10.1016/j.str.2023.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 02/22/2023] [Accepted: 04/19/2023] [Indexed: 05/18/2023]
Abstract
The coordinated release of Ca2+ from the sarcoplasmic reticulum (SR) is critical for excitation-contraction coupling. This release is facilitated by ryanodine receptors (RyRs) that are embedded in the SR membrane. In skeletal muscle, activity of RyR1 is regulated by metabolites such as ATP, which upon binding increase channel open probability (Po). To obtain structural insights into the mechanism of RyR1 priming by ATP, we determined several cryo-EM structures of RyR1 bound individually to ATP-γ-S, ADP, AMP, adenosine, adenine, and cAMP. We demonstrate that adenine and adenosine bind RyR1, but AMP is the smallest ATP derivative capable of inducing long-range (>170 Å) structural rearrangements associated with channel activation, establishing a structural basis for key binding site interactions that are the threshold for triggering quaternary structural changes. Our finding that cAMP also induces these structural changes and results in increased channel opening suggests its potential role as an endogenous modulator of RyR1 conductance.
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Affiliation(s)
- Spencer Cholak
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - James W Saville
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Xing Zhu
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Alison M Berezuk
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Katharine S Tuttle
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Omid Haji-Ghassemi
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Francisco J Alvarado
- Department of Medicine and Cardiovascular Research Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Sriram Subramaniam
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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3
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Saville JW, Mannar D, Zhu X, Berezuk AM, Cholak S, Tuttle KS, Vahdatihassani F, Subramaniam S. Structural analysis of receptor engagement and antigenic drift within the BA.2 spike protein. Cell Rep 2023; 42:111964. [PMID: 36640338 PMCID: PMC9812370 DOI: 10.1016/j.celrep.2022.111964] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/10/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
The BA.2 sub-lineage of the Omicron (B.1.1.529) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant rapidly supplanted the original BA.1 sub-lineage in early 2022. Both lineages threatened the efficacy of vaccine-elicited antibodies and acquired increased binding to several mammalian ACE2 receptors. Cryoelectron microscopy (cryo-EM) analysis of the BA.2 spike (S) glycoprotein in complex with mouse ACE2 (mACE2) identifies BA.1- and BA.2-mutated residues Q493R, N501Y, and Y505H as complementing non-conserved residues between human and mouse ACE2, rationalizing the enhanced S protein-mACE2 interaction for Omicron variants. Cryo-EM structures of the BA.2 S-human ACE2 complex and of the extensively mutated BA.2 amino-terminal domain (NTD) reveal a dramatic reorganization of the highly antigenic N1 loop into a β-strand, providing an explanation for decreased binding of the BA.2 S protein to antibodies isolated from BA.1-convalescent patients. Our analysis reveals structural mechanisms underlying the antigenic drift in the rapidly evolving Omicron variant landscape.
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Affiliation(s)
- James W. Saville
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Dhiraj Mannar
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Xing Zhu
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Alison M. Berezuk
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Spencer Cholak
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Katharine S. Tuttle
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Faezeh Vahdatihassani
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Sriram Subramaniam
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada,Gandeeva Therapeutics, Inc., Burnaby, BC V5C 6N5, Canada,Corresponding author
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4
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Saville JW, Berezuk AM, Srivastava SS, Subramaniam S. Three-Dimensional Visualization of Viral Structure, Entry, and Replication Underlying the Spread of SARS-CoV-2. Chem Rev 2022; 122:14066-14084. [PMID: 35863749 PMCID: PMC9344915 DOI: 10.1021/acs.chemrev.1c01062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
![]()
The global spread
of SARS-CoV-2 has proceeded at an unprecedented
rate. Remarkably, characterization of the virus using modern tools
in structural biology has also progressed at exceptional speed. Advances
in electron-based imaging techniques, combined with decades of foundational
studies on related viruses, have enabled the research community to
rapidly investigate structural aspects of the novel coronavirus from
the level of individual viral proteins to imaging the whole virus
in a native context. Here, we provide a detailed review of the structural
biology and pathobiology of SARS-CoV-2 as it relates to all facets
of the viral life cycle, including cell entry, replication, and three-dimensional
(3D) packaging based on insights obtained from X-ray crystallography,
cryo-electron tomography, and single-particle cryo-electron microscopy.
The structural comparison between SARS-CoV-2 and the related earlier
viruses SARS-CoV and MERS-CoV is a common thread throughout this review.
We conclude by highlighting some of the outstanding unanswered structural
questions and underscore areas that are under rapid current development
such as the design of effective therapeutics that block viral infection.
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Affiliation(s)
- James W Saville
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3
| | - Alison M Berezuk
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3
| | - Shanti S Srivastava
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3
| | - Sriram Subramaniam
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3.,Gandeeva Therapeutics Inc., Vancouver, British Columbia, Canada, V5C 6N5
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5
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Chen C, Saville JW, Marti MM, Schäfer A, Cheng MH, Mannar D, Zhu X, Berezuk AM, Banerjee A, Sobolewski MD, Kim A, Treat BR, Da Silva Castanha PM, Enick N, McCormick KD, Liu X, Adams C, Hines MG, Sun Z, Chen W, Jacobs JL, Barratt-Boyes SM, Mellors JW, Baric RS, Bahar I, Dimitrov DS, Subramaniam S, Martinez DR, Li W. Potent Neutralization of Omicron and other SARS-CoV-2 Variants of Concern by Biparatopic Human VH Domains. bioRxiv 2022:2022.02.18.481058. [PMID: 35194603 PMCID: PMC8863138 DOI: 10.1101/2022.02.18.481058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The emergence of SARS-CoV-2 variants of concern (VOCs) requires the development of next-generation biologics that are effective against a variety of strains of the virus. Herein, we characterize a human V H domain, F6, which we generated by sequentially panning large phage displayed V H libraries against receptor binding domains (RBDs) containing VOC mutations. Cryo-EM analyses reveal that F6 has a unique binding mode that spans a broad surface of the RBD and involves the antibody framework region. Attachment of an Fc region to a fusion of F6 and ab8, a previously characterized V H domain, resulted in a construct (F6-ab8-Fc) that neutralized Omicron pseudoviruses with a half-maximal neutralizing concentration (IC 50 ) of 4.8 nM in vitro . Additionally, prophylactic treatment using F6-ab8-Fc reduced live Beta (B.1.351) variant viral titers in the lungs of a mouse model. Our results provide a new potential therapeutic against SARS-CoV-2 VOCs - including the recently emerged Omicron variant - and highlight a vulnerable epitope within the spike protein RBD that may be exploited to achieve broad protection against circulating variants.
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Affiliation(s)
- Chuan Chen
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA
| | - James W. Saville
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver BC, V6T 1Z3
| | - Michelle M. Marti
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3109 Michael Hooker Research Center, Chapel Hill, NC 27599, USA
| | - Mary Hongying Cheng
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dhiraj Mannar
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver BC, V6T 1Z3
| | - Xing Zhu
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver BC, V6T 1Z3
| | - Alison M. Berezuk
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver BC, V6T 1Z3
| | - Anupam Banerjee
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michele D. Sobolewski
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Andrew Kim
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA
| | - Benjamin R. Treat
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Priscila Mayrelle Da Silva Castanha
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Nathan Enick
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Kevin D McCormick
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Xianglei Liu
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA
| | - Cynthia Adams
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA
| | - Margaret Grace Hines
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA
| | - Zehua Sun
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA
| | | | - Jana L. Jacobs
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Simon M. Barratt-Boyes
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - John W. Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America,Abound Bio, Pittsburgh, PA, USA
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3109 Michael Hooker Research Center, Chapel Hill, NC 27599, USA
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dimiter S. Dimitrov
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA,Abound Bio, Pittsburgh, PA, USA,Correspondence: , , and
| | - Sriram Subramaniam
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver BC, V6T 1Z3,Correspondence: , , and
| | - David R. Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3109 Michael Hooker Research Center, Chapel Hill, NC 27599, USA,Correspondence: , , and
| | - Wei Li
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA,Correspondence: , , and
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6
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Mannar D, Saville JW, Zhu X, Srivastava SS, Berezuk AM, Tuttle KS, Marquez AC, Sekirov I, Subramaniam S. SARS-CoV-2 Omicron variant: Antibody evasion and cryo-EM structure of spike protein-ACE2 complex. Science 2022; 375:760-764. [PMID: 35050643 DOI: 10.1101/2021.12.19.473380] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The newly reported Omicron variant is poised to replace Delta as the most prevalent SARS-CoV-2 variant across the world. Cryo-EM structural analysis of the Omicron variant spike protein in complex with human ACE2 reveals new salt bridges and hydrogen bonds formed by mutated residues R493, S496 and R498 in the RBD with ACE2. These interactions appear to compensate for other Omicron mutations such as K417N known to reduce ACE2 binding affinity, resulting in similar biochemical ACE2 binding affinities for Delta and Omicron variants. Neutralization assays show that pseudoviruses displaying the Omicron spike protein exhibit increased antibody evasion. The increase in antibody evasion, together with retention of strong interactions at the ACE2 interface, thus represent important molecular features that likely contribute to the rapid spread of the Omicron variant.
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MESH Headings
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/metabolism
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- COVID-19/immunology
- COVID-19 Vaccines/immunology
- Cryoelectron Microscopy
- Humans
- Hydrogen Bonding
- Immune Evasion
- Models, Molecular
- Mutation
- Neutralization Tests
- Protein Binding
- Protein Domains
- Protein Interaction Domains and Motifs
- Receptors, Coronavirus/chemistry
- Receptors, Coronavirus/metabolism
- SARS-CoV-2/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
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Affiliation(s)
- Dhiraj Mannar
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - James W Saville
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Xing Zhu
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Shanti S Srivastava
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Alison M Berezuk
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Katharine S Tuttle
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Ana Citlali Marquez
- BC Center for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Inna Sekirov
- BC Center for Disease Control Public Health Laboratory, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Sriram Subramaniam
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
- Gandeeva Therapeutics, Inc., Vancouver, BC, Canada
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7
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Mannar D, Saville JW, Zhu X, Srivastava SS, Berezuk AM, Tuttle KS, Marquez AC, Sekirov I, Subramaniam S. SARS-CoV-2 Omicron variant: Antibody evasion and cryo-EM structure of spike protein-ACE2 complex. Science 2022; 375:760-764. [PMID: 35050643 DOI: 10.1126/science.abn7760] [Citation(s) in RCA: 368] [Impact Index Per Article: 184.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Dhiraj Mannar
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - James W Saville
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Xing Zhu
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Shanti S Srivastava
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Alison M Berezuk
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Katharine S Tuttle
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Ana Citlali Marquez
- BC Center for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Inna Sekirov
- BC Center for Disease Control Public Health Laboratory, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Sriram Subramaniam
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.,Gandeeva Therapeutics, Inc., Vancouver, BC, Canada
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8
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Zhu X, Mannar D, Srivastava SS, Berezuk AM, Demers JP, Saville JW, Leopold K, Li W, Dimitrov DS, Tuttle KS, Zhou S, Chittori S, Subramaniam S. Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. PLoS Biol 2021; 19:e3001237. [PMID: 33914735 PMCID: PMC8112707 DOI: 10.1371/journal.pbio.3001237] [Citation(s) in RCA: 137] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/11/2021] [Accepted: 04/16/2021] [Indexed: 12/15/2022] Open
Abstract
The recently reported "UK variant" (B.1.1.7) of SARS-CoV-2 is thought to be more infectious than previously circulating strains as a result of several changes, including the N501Y mutation. We present a 2.9-Å resolution cryo-electron microscopy (cryo-EM) structure of the complex between the ACE2 receptor and N501Y spike protein ectodomains that shows Y501 inserted into a cavity at the binding interface near Y41 of ACE2. This additional interaction provides a structural explanation for the increased ACE2 affinity of the N501Y mutant, and likely contributes to its increased infectivity. However, this mutation does not result in large structural changes, enabling important neutralization epitopes to be retained in the spike receptor binding domain. We confirmed this through biophysical assays and by determining cryo-EM structures of spike protein ectodomains bound to 2 representative potent neutralizing antibody fragments.
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Affiliation(s)
- Xing Zhu
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dhiraj Mannar
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shanti S. Srivastava
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alison M. Berezuk
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jean-Philippe Demers
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - James W. Saville
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Karoline Leopold
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wei Li
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania, United States of America
| | - Dimiter S. Dimitrov
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania, United States of America
| | - Katharine S. Tuttle
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven Zhou
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sagar Chittori
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sriram Subramaniam
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
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9
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Saville JW, Ross JA, Trefz T, Schatz C, Matheson-Bird H, Ralston B, Granot O, Schmid K, Terry R, Allan ND, Wulff JE, Olson M. Development and Field Validation of Lidocaine-Loaded Castration Bands for Bovine Pain Mitigation. Animals (Basel) 2020; 10:ani10122363. [PMID: 33321859 PMCID: PMC7763166 DOI: 10.3390/ani10122363] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Castration is among the most common management procedures performed in the dairy and beef cattle industries. Despite the widely accepted benefits of castration, all castration methods produce pain and distress. While slower than other approaches, castration by banding is simple, inexpensive, and produces fewer complications. We have therefore focused the present study on developing herd-level pain mitigation during banded castration. Because lidocaine is effective at reducing pain and can be delivered topically, we have formulated lidocaine-loaded castration bands (LLBs) to deliver local pain relief to calves and bulls during banded castration. Laboratory results indicated a rapid release of lidocaine for the first 30 min, followed by a slow release for at least 48 h. Field studies indicated that, for both lidocaine delivery into tissues and pain mitigation, LLBs performed at least as well as standard lidocaine injections in the short term and outperformed lidocaine injections in the long term. LLBs delivered therapeutic quantities of lidocaine into scrotal tissues over a period of at least seven days in cattle. This approach would provide long-term pain mitigation to the animals and, by avoiding surgery or the administration of injections, would also decrease the time and handling costs for the producer. Abstract Castration is among the most common management procedures performed in the dairy and beef cattle industries and is mainly performed by surgery or elastic banding. Despite the various benefits of castration, all methods produce pain and distress. Castration by banding is simple, inexpensive, produces fewer complications, and can be performed in a high-throughput manner. Because lidocaine, a local anesthetic, can be delivered to trauma sites topically, we have formulated lidocaine-loaded castration bands (LLBs) to deliver local pain relief to calves during banded castration. The initial lidocaine content of three band types developed was between 80 and 200 mg per band. The transfer kinetics of lidocaine into tissue was determined in vitro, indicating a rapid release for the first 30 min, followed by a slow release lasting at least 48 h. Furthermore, the lidocaine delivery and pain mitigation effects of these LLBs were compared to standard lidocaine injections in vivo. Field studies indicated that LLBs performed at least as well as lidocaine injections for short-term lidocaine delivery into tissues and pain mitigation. Moreover, LLBs significantly outperformed lidocaine injections for long-term delivery and pain mitigation. The concentrations of lidocaine in the LLB-treated tissue samples were generally in the range of 0.5–3.5 mg of lidocaine per gram of tissue and were overall highest after 6 h. Lidocaine-loaded elastration bands deliver therapeutic quantities of lidocaine into scrotal tissues over a period of at least seven days in cattle. This approach would provide long-term pain mitigation to the animals and, by avoiding surgery or the administration of injections, would also decrease the time and handling costs for the producer.
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Affiliation(s)
- James W. Saville
- Department of Chemistry, University of Victoria, Victoria, BC V8W 3V6, Canada; (J.W.S.); (T.T.); (O.G.)
| | - Joseph A. Ross
- Chinook Contract Research Inc., Airdrie, AB T4A 0C3, Canada; (J.A.R.); (C.S.); (H.M.-B.)
| | - Tyler Trefz
- Department of Chemistry, University of Victoria, Victoria, BC V8W 3V6, Canada; (J.W.S.); (T.T.); (O.G.)
| | - Crystal Schatz
- Chinook Contract Research Inc., Airdrie, AB T4A 0C3, Canada; (J.A.R.); (C.S.); (H.M.-B.)
| | - Heather Matheson-Bird
- Chinook Contract Research Inc., Airdrie, AB T4A 0C3, Canada; (J.A.R.); (C.S.); (H.M.-B.)
| | - Brenda Ralston
- Alberta Agriculture and Forestry, Airdrie, AB T4A 0C3, Canada;
| | - Ori Granot
- Department of Chemistry, University of Victoria, Victoria, BC V8W 3V6, Canada; (J.W.S.); (T.T.); (O.G.)
| | - Karin Schmid
- Alberta Beef Producers, Calgary, AB T2E 7H7, Canada;
| | - Richard Terry
- Richard Terry Innovations, LLC, Conyers, GA 30094, USA;
| | - Nicholas D. Allan
- Chinook Contract Research Inc., Airdrie, AB T4A 0C3, Canada; (J.A.R.); (C.S.); (H.M.-B.)
- Correspondence: (N.D.A.); (J.E.W.)
| | - Jeremy E. Wulff
- Department of Chemistry, University of Victoria, Victoria, BC V8W 3V6, Canada; (J.W.S.); (T.T.); (O.G.)
- Correspondence: (N.D.A.); (J.E.W.)
| | - Merle Olson
- Alberta Veterinary Laboratories, Calgary, AB T2C 5N6, Canada;
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Saville JW, Troman L, Duong Van Hoa F. PeptiQuick, a One-Step Incorporation of Membrane Proteins into Biotinylated Peptidiscs for Streamlined Protein Binding Assays. J Vis Exp 2019. [PMID: 31736482 DOI: 10.3791/60661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Membrane proteins, including transporters, channels, and receptors, constitute nearly one-fourth of the cellular proteome and over half of current drug targets. Yet, a major barrier to their characterization and exploitation in academic or industrial settings is that most biochemical, biophysical, and drug screening strategies require these proteins to be in a water-soluble state. Our laboratory recently developed the peptidisc, a membrane mimetic offering a "one-size-fits-all" approach to the problem of membrane protein solubility. We present here a streamlined protocol that combines protein purification and peptidisc reconstitution in a single chromatographic step. This workflow, termed PeptiQuick, allows for bypassing dialysis and incubation with polystyrene beads, thereby greatly reducing exposure to detergent, protein denaturation, and sample loss. When PeptiQuick is performed with biotinylated scaffolds, the preparation can be directly attached to streptavidin-coated surfaces. There is no need to biotinylate or modify the membrane protein target. PeptiQuick is showcased here with the membrane receptor FhuA and antimicrobial ligand colicin M, using biolayer interferometry to determine the precise kinetics of their interaction. It is concluded that PeptiQuick is a convenient way to prepare and analyze membrane protein-ligand interactions within one day in a detergent-free environment.
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Affiliation(s)
| | - Lucy Troman
- School of Biochemistry, University of Bristol
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Gray PA, Saville JW, Krause KD, Burford N, McDonald R, Ferguson MJ. [GaX 2(dmpe) 2][GaX 4] (X = Cl, Br, I): a synthetic, solid state, and computational study. CAN J CHEM 2017. [DOI: 10.1139/cjc-2016-0469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Derivatives of [GaX2(dmpe)2][GaX4] (X = Cl,Br, I) were prepared and characterized. The salts contain a cation involving two diphosphine ligands bound to GaX2+, imposing a pseudo-octahedral geometry at gallium. A variety of possible structural alternatives for the equimolar combination of GaX3 and dmpe have been computationally modelled and shown to be energetically similar to the observed cations, indicating potential fluxionality in the system, and are in agreement with spectroscopic characterization.
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Affiliation(s)
- Paul A. Gray
- Department of Chemistry, University of Victoria, Victoria, BC V8W 3V6, Canada
| | - James W. Saville
- Department of Chemistry, University of Victoria, Victoria, BC V8W 3V6, Canada
| | - Katherine D. Krause
- Department of Chemistry, University of Victoria, Victoria, BC V8W 3V6, Canada
| | - Neil Burford
- Department of Chemistry, University of Victoria, Victoria, BC V8W 3V6, Canada
| | - Robert McDonald
- X-ray Crystallography Laboratory, Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Michael J. Ferguson
- X-ray Crystallography Laboratory, Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
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